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I read about the regulation of Calvin cycle by thioredoxin which activates key enzymes essentially by converting disulphide linkages on inactive enzymes into sulfhydryls. Another regulatory mechanism is the pH control. The enzymes work at a slightly alkaline pH which is established as soon as the proton gradient is set up by the light reactions. But aren't these two mechanisms contradictory: at alkaline pH, the sulfhydryls $-SH$ groups, being acidic, will dissociate by giving up a proton and will be more stable in the dissociated form.
In general I fail to understand how pH will decide which bio-compounds will dissociate into proton or hydroxyl.

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up vote 4 down vote accepted

Your question conflates two separable events, a redox process and an acid-base dissociation.

The interconversion between disulfides and free sulfhydryls is a redox reaction, governed by the redox potential of the surroundings. The importance of redox potential to the -S-S- <> -SH equilibrium is illustrated by the difference between the cytosol and the lumen of the endoplasmic reticulum (ER). The cytosol is reducing and so free thiols are prevalent (there are usually no disulfide bonds in cytosolic proteins) whereas the ER lumen is oxidising, and the formation of disulfides in secreted proteins is promoted. The redox potentials of the two compartments is set primarily by the ratio between oxidised glutathione and reduced glutathione.

The thiol group in cysteine residues of proteins typically has a pKa of around 7, so it will indeed have some acidic character at slightly alkaline pH, dissociating to form a thiolate group. This doesn't however promote the reformation of disulfides, and in any case if it is important for a protein to have an undissociated thiol, then the environment of the specific cysteine residue can be adapted to raise its pKa. Note however that it is also possible that the thiolate form may be compatible with (or even required for) the function of the enzyme.

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